I usually leave all my escorts and frigates on auto, the AI does a good job assigning them to escort duty and so protects my mining fleet. Bases get designed in a way that they can handle themselves. (~10 weapon systems of choice, more shields) In addition at midgame I build and assign small destroyer fleets and assign them defense stance and so cover my territory. This seems to protect my assets well enough. The occasional pirate still slips through, but that is inevitable.